When you initially duplicate the DB, your character will be copied over. You are right though that you have essentially created a separate server and any progress you make thereafter on either server will not show up on the other. That's just the reality of having two databases. You could alter the code to always point to one set of character data, but that would be somewhat complex and could introduce new issues. Or you can continue to dump and copy character data between instances, though obviously that is manually burdensome. But those are your options if you want two databases.
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